The new club started at the very bottom of the Finnish football pyramid, spending their first years in the fifth and sixth divisions.

[1] With the new organisation in place, the football club started to enjoy some success in the third division, and were promoted back to the Kakkonen for the 2001 season.

In the following season, he led the club to first place in the Ykkönen, winning promotion to the Veikkausliiga, the highest level of Finnish football.

In the first ever premier division match played at Heteniitty, Viikingit beat FC Honka with a 3–2 scoreline and an attendance of over 3,000.

The attendance record, which is still in force, was created in the local derby against HJK Helsinki, which drew 4,255 viewers to Vuosaaren urheilukenttä.

In 2008, the new manager Toni Korkeakunnas led the team to second place, but KuPS took the promotion play-off with an aggregate scoreline of 2–1.

[1] The club's attendance record in the Ykkönen, 1,670 viewers, was created on 21 July 2011 against local rivals HIFK.

[2] In 2013, the club were in danger of relegation to the Kakkonen, but played well in the closing stage of the season, finishing seventh in the end.

[4] FC Viikingit play their home matches at Vuosaaren urheilukenttä, often called Heteniitty or Hettari.

The reserve side FC Viikkarit play their home matches at Kartanon kenttä in Nordsjön kartano.

[5] Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.